Japanese place names include names for geographic features, present and former administrative divisions, transportation facilities such as railroad stations, and historic sites in Japan. The article Japanese addressing system contains related information on postal addresses.

-fu (府, lit. "office" or "area"), prefecture-level region (sometimes translated "urban prefecture") named so for historical reasons. There are now only two: Ōsaka-fu and Kyōto-fu. Tokyo-to was also classified as this before being reorganized.

dō (道), an "administrative circuit", a semi-archaic administrative division formerly widespread. Modern usage is limited to Hokkaido, but terms like Tōkaidō (southern portion of eastern Japan) remains in common informal usage.

Because of the above four suffixes, the prefectures of Japan are commonly referred to as todōfuken (都道府県). And below the level of prefectures, there are:

Medieval Japan had many towns that fell into three categories: castle towns, post towns, harbor towns. In addition, the rise of commerce contributed to some place names. Here are some parts of names connected with medieval Japan:

Many names in Hokkaido originated from words in the Ainu language, as people from mainland Japan conquered and colonized Hokkaido in the Edo period and the Meiji period. Examples of geographic features are -nai and -betsu meaning "river", as in the names Wakkanai and Noboribetsu. The name Esashi comes from the Ainu word esaushi, meaning "cape." Some other names come from places in other parts of Japan because in the past people migrated as a group to Hokkaido, and they give the new settlement a name reminiscent of their old home. Examples include Hiroshima and Date, Hokkaido.

During the rule of the Shoguns (1185-1867), families of samurai often adopted place names as their surnames. Examples are the Ashikaga clan and the Taira clan.

Place names in Okinawa Prefecture are drawn from the traditional Ryukyuan languages. Many place names use the unique languages names, while other place names have both a method of reading the name in Japanese and a way to read the name in one of the traditional local languages. The capital city Naha is Naafa in the Okinawan language. Uruma, which was incorporated in 2005, comes from an old name for the Okinawa Island meaning "coral island" and its name is written in hiragana rather than kanji. In Okinawan, nishi meant "north" rather than "west" as it does in standard Japanese, so Nishihara means "northern field" in respect to its position from the old Ryūkyū Kingdom capital at Shuri; in contrast, the Okinawan word for "west" is iri, which appears in the name of Iriomote-jima. Gusuku (城) meaning "castle" is also common in place names in Okinawa, found in Tomigusuku, Nakagusuku, and Kitanakagusuku, among others. Both Chatan and Yomitan turn tani (谷, "valley") into tan; Chatan also turns kita (北) into "cha" through the Okinawan language.

Shin Nihon chimei sakuin (新日本地名索引, 1993 New Index Gazetteer of Japan) Abokkusha. This is the most comprehensive dictionary for reading place names. Each entry simply lists the reading of place name, its kanji, location, and longitude-latitude coordinate.

Dai Nihon Chimei Jisho (大日本地名辞書) is one of oldest, in 1907-1910, reprint and update version by 1971, published by Buzanbō (富山房). The main editor was Tōgo Yoshida (吉田 東伍,1864-1918） written in vernacular expression in Meiji period with each entry includes the history and folklore for name.

Kadokawa Nihon chimei daijiten (角川日本地名大辞典) Kadokawa Shoten, published in the 1970s-1980s. This is the major encyclopedia for Japanese geographic reference. Each entry includes the history of the place, its population, major happenings in the place, and major buildings such as schools, temples, and churches among others.

Konpakutoban Nihon chimei hyakka jiten (コンパクト版日本地名百科事典, Compact Land Japonica) Shogakukan in June 1998. This is the desktop dictionary for geographic reference. It is designed to be easily comprehensible. It includes color maps of entire Japan and detail maps of major Japanese cities; Tokyo, Kyoto-shi, Nara-shi, Osaka-shi, and Nagoya-shi. The index for hard-to-read place names is included at the back of the dictionary.

Kodai chimei daijiten (古代地名大辞典) Kadokawa Shoten This work lists in gojuon order the place names of ancient Japanese history. The periods range from the Asuka period (飛鳥時代, Asuka-jidai, 538-710), Nara period (奈良時代, Nara-jidai, 710-794), and Heian period (平安時代, Heian-jidai, 710-1185). It especially focuses on the place names from the Man'yōshū (万葉集) poetry anthology and the Fudoki (風土記) chronicles.

Nihon chimei gogen jiten (日本地名語源事典) Shinjinbutsu oraisha Based on the studies of geography and Japanese ancient words, each entry lists a few sentences about the origin and history of place names in gojuon order.